Structure of PDB 7bzj Chain A Binding Site BS01

Receptor Information
>7bzj Chain A (length=183) Species: 561276 (Streptococcus pneumoniae ATCC 700669) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TGANVTFKVKGTDKEFTVFTTRPDTLFGATFTVLAPEHELVDAITSSEQA
EAVADYKHQASLKSDLVRTDLAKEKTGVWTGAYAINPVNGKEMPIWIADY
VLASYGTGAVMAVPAHDQRDWEFAKQFDLPIVEVLEGGNVEEAAYTEDGL
HVNSDFLDGLNKEDAIAKIVASLEEKGCGQEKV
Ligand information
Ligand IDFGX
InChIInChI=1S/C28H31BN5O9PS/c1-15(35)12-45-19-6-4-17(5-7-19)23(36)18-3-2-16-8-9-29(20(16)10-18)42-24-21(11-40-44(37,38)39)41-28(25(24)43-29)34-14-33-22-26(30)31-13-32-27(22)34/h2-7,10,13-14,21,23-25,28,36-39H,8-9,11-12H2,1H3,(H2,30,31,32)/t21-,23+,24-,25+,28+,29+/m0/s1
InChIKeyYYNKFKBRIAWSCO-QTPLPVLTSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(=O)CSc1ccc(cc1)[CH](O)c2ccc3CC[B-]4(O[CH]5[CH](CO[P+](O)(O)O)O[CH]([CH]5O4)n6cnc7c(N)ncnc67)c3c2
CACTVS 3.385CC(=O)CSc1ccc(cc1)[C@@H](O)c2ccc3CC[B-]4(O[C@H]5[C@H](CO[P+](O)(O)O)O[C@H]([C@@H]5O4)n6cnc7c(N)ncnc67)c3c2
OpenEye OEToolkits 2.0.7[B-]12(CCc3c1cc(cc3)C(c4ccc(cc4)SCC(=O)C)O)OC5C(OC(C5O2)n6cnc7c6ncnc7N)CO[P+](O)(O)O
OpenEye OEToolkits 2.0.7[B-]12(CCc3c1cc(cc3)[C@@H](c4ccc(cc4)SCC(=O)C)O)O[C@H]5[C@@H](O[C@H]([C@@H]5O2)n6cnc7c6ncnc7N)CO[P+](O)(O)O
FormulaC28 H31 B N5 O9 P S
Name[(1~{R},5~{R},6~{S},8~{R})-8-(6-aminopurin-9-yl)-4'-[(~{R})-oxidanyl-[4-(2-oxidanylidenepropylsulfanyl)phenyl]methyl]spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,7'-7-boranuidabicyclo[4.3.0]nona-1(6),2,4-triene]-6-yl]methoxy-tris(oxidanyl)phosphanium
ChEMBL
DrugBank
ZINC
PDB chain7bzj Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7bzj Discovery of benzhydrol-oxaborole derivatives as Streptococcus pneumoniae leucyl-tRNA synthetase inhibitors.
Resolution2.0 Å
Binding residue
(original residue number in PDB)
T247 T248 R249 V328 L329 Y332 V337 M338 H343 D344 K389
Binding residue
(residue number reindexed from 1)
T20 T21 R22 V101 L102 Y105 V110 M111 H116 D117 K162
Annotation score1
Enzymatic activity
Enzyme Commision number 6.1.1.4: leucine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0002161 aminoacyl-tRNA editing activity
GO:0004823 leucine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006429 leucyl-tRNA aminoacylation

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Molecular Function

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Biological Process
External links
PDB RCSB:7bzj, PDBe:7bzj, PDBj:7bzj
PDBsum7bzj
PubMed33221064
UniProtB8ZKS5|SYL_STRPJ Leucine--tRNA ligase (Gene Name=leuS)

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